Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 559 records · Page 31Linked to original sources

bioRxiv2019

REC8-cohesin, chromatin and transcription orchestrate meiotic recombination in the Arabidopsis genome

During meiosis chromosomes undergo DNA double-strand breaks (DSBs) that can be repaired using a homolog to produce crossovers, which creates genetic diversity. Meiotic recombination occurs coincident with homolog pairing and polymerization of the meiotic axis and synaptonemal complex (SC). REC8-cohesin is required to connect chromosomes to the axis and to organize axis polymerization. However, control of REC8 loading along chromosomes, in relation to chromatin, transcription and recombination, is not yet fully understood. Therefore, we performed REC8 ChIP-seq in Arabidopsis, which revealed strong enrichment in centromeric heterochromatin. REC8 abundance correlates with suppression of meiotic DSBs and crossovers, despite axis loading of SPO11-1 in these regions. Loss of the heterochromatic marks H3K9me2 and non-CG DNA methylation in kyp/suvh4 suvh5 suvh6 mutants causes remodeling of REC8 and gain of meiotic recombination locally in repeated sequences, although centromere cohesion is maintained. In the chromosome arms, REC8 is enriched within gene bodies, exons and GC-rich sequences, and anti-correlates with transcription. Highest REC8 occupancy occurred in facultatively silent, H3K27me3-modified genes. Using immunocytology we show that axis polycomplexes form in rec8 mutants that recruit recombination foci with altered stoichiometry, leading to catastrophic non-homologous recombination. Therefore, REC8 plays a key role organizing meiotic chromosome architecture and promoting high-fidelity interhomolog recombination. Despite this pro-recombination role, local REC8 enrichment associates with DSB repression at the fine scale, which is consistent with the tethered-loop/axis model. Coincident with its organizational role during meiosis, REC8-cohesin occupancy along the chromosomes is shaped by multiple chromatin states and transcription.

genomics↗

bioRxiv2018

WBC-Profiler: an Unsupervised Feature Learning System for Leukocytes Characterization and Classification

The characterization and classification of white blood cells (WBC) is critical for the diagnosis of anemia, leukemia and many other hematologic diseases. We developed WBC-Profiler, an unsupervised feature learning system for quantitative analysis of leukocytes. We demonstrate that WBC-Profiler enables automatic extraction of complex signatures from microscopic images without human-intervention and thereafter effective construction of leukocytes profiles, which decouples large scale complex leukocytes characterization from limitations in both human-based feature engineering/optimization and the end-to-end solutions provided by modern deep neural networks, and therefore has the potential to provide new opportunities towards meaningful studies/applications with scientific and/or clinical impact

bioinformatics↗

bioRxiv2018

Whole-tree heartwood inducing technique for Dalbergia odorifera

The dried heartwood of Dalbergia odorifera is a very important traditional Chinese medicine. In nature, D. odorifera heartwood forms slowly over several decades, and excessive harvesting has caused large-scale reductions of its wild populations. To date, there have been no studies on artificial methods to induce heartwood formation in trees that have not already begun producing heartwood. We have published a patent for a whole-tree heartwood inducing technique for D. odorifera (the \"Dodor-Wit\" method); here, we describe and analyze its efficacy. Trees in four plantations in China were treated using this method. After two years, in 2016 and 2017, they were harvested and analyzed. Average heartwood yield per tree was 3,161.95 g. Heartwood induction rate (dry heartwood weight to total dry trunk weight after peeling) was 21.60%. Average volatile oil content per tree was 1.42%. Alcohol-soluble extract of the induced heartwood was 15.77%, exceeding the Chinese Pharmacopoeia standard. This is the first report on the Dodor-Wit method and heartwood induction in D. odorifera trees aged 5-8 years. The heartwood induced by Dodor-Wit satisfies the requirements of the Chinese Pharmacopoeia. The Dodor-Wit method has an important role in solving the extreme scarcity of Chinese medicinal herbs.

plant biology↗

bioRxiv2018

Decreased metabolism and increased tolerability to extreme environment in Staphylococcus warneri with long-term space flight

BackgroundMany studies have shown that space environment can affect bacteria to cause a range of mutations. However, so far, there are less studies on the effects of long-term space flight (>1 month) on bacteria. In this study, a Staphylococcus warneri strain, which was isolated from the Shenzhou-10 spacecraft that had experienced a space flight (15-day), was carried into space again. After 64-day flight, the combined phenotypic, genomic, transcriptomic and proteomic analyses were performed to compare the influence of the two space flights on this bacteria.\n\nResultsCompared with short-term space flight, long-term space flight increased the biofilm formation ability of S. warneri and the cell wall resistance to external environment stress, but reduced the sensitivity to chemical stimulation. Further analysis showed that these changes might be related to the significantly up-regulated gene expression of phosphotransferase system, which regulated glucose metabolism pathway, including glucose, mannose, fructose and cellobiose. The mutation of S. warneri caused by 15-day space flight was limited at phenotype and gene level after ground culture.\n\nConclusionAfter a 79-day space flight, the changes of S. warneri are meaningful. Phosphotransferase system of S. warneri was up-regulated by long-term space stimulation, which resulted in a series of changes in cell wall, biofilm and chemical sensitivity, thus enhancing the resistance and adaptability of bacteria to the external environment.\n\nImportanceTaking S. warneri as an example, we found that the mutation of bacteria in long-term space flight mainly focused on the adaptation and tolerance like environmental adaptation, physical resistance and cell repair to various pressures and these changes should be more obvious or even become stable mutations. But the clinical changes, for example drug resistance and virulence should not be significant because there is no threat of antibiotics.

microbiology↗

bioRxiv2018

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

genomics↗

bioRxiv2018

The landscapes of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight to embryonic muscle development in chicken

As DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, by constructing the network of the lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.

bioinformatics↗

bioRxiv2018

A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance

The introgression of a small segment of wheat chromosome 1BS in the distal region of the rye 1RS arm translocation in wheat (henceforth 1RSrw) was previously associated with reduced grain yield, carbon isotope discrimination and stomatal conductance, suggesting reduced access to soil moisture. In this study, we show that the 1RS/1RSRW polymorphism causes differences in root length in field and hydroponic experiments. In the latter, differences in seminal root length were associated with a developmentally regulated arrest of the root apical meristem (RAM). Approximately 10 days after germination, the seminal roots of the 1RSRW plants showed a gradual reduction in elongation rate and stopped growing a week later. Seventeen days after germination, the roots of the 1RSRW plants showed altered gradients of reactive oxygen species and emergence of lateral roots close to the RAM, suggesting a loss of apical dominance. The 1RS/1RSRW isogenic lines also differed in plant biomass and grain yield under normal, terminal drought, and waterlogging field conditions. The differences were larger in fields with reduced or excessive irrigation. These results suggest that this polymorphism may be useful to modulate root architecture and mitigate the negative impacts of excess or reduced water in wheat production.\n\nHIGHLIGHTA wheat/rye polymorphism in chromosome one affects seminal root length and apical dominance and is associated with differences in drought and waterlogging tolerance in the field.

plant biology↗

bioRxiv2018

The LIM-Only Protein FHL2 is Involved in Autophagy to Regulate the Development of Skeletal Muscle

Four and a half LIM domain protein 2 (FHL2) is a LIM domain protein expressed in muscle tissue whose deletion is causative of myopathies. Although FHL2 has a confirmed important role in muscle development, its autophagy-related function in muscle differentiation has not been fully determined. To explore the role of FHL2 in autophagy-related muscle regulation, FHL2-silenced and -overexpressing C2C12 mouse cells were examined. Immunofluorescence and co-immunoprecipitation assay findings showed that FHL2 silencing reduced LC3- protein expression and the amount of LC3 that co-immunoprecipitated with FHL2, indicating that FHL2 interacts with LC3- in the formation of autophagosomes. Moreover, the expression of muscle development marker genes such as MyoD1 and MyoG was lower in FHL2-silenced C2C12 cells but not in FHL2-overexpressing C2C12 cells. Electron microscopy analysis revealed large empty autophagosomes in FHL2-silenced myoblasts, while flow cytometry suggested that FHL2 silencing made cells more vulnerable to staurosporine-induced cell death. In conclusion, we propose that FHL2 interacts with LC3- in autophagosome formation to regulate the development of muscle cells.

molecular biology↗

bioRxiv2018

HiAlc Klebsiella pneumonia, one of potential chief culprits of non-alcoholic fatty liver disease: through generation of endogenous ethanol

Non-alcoholic fatty liver disease (NAFLD), a prelude of cirrhosis and hepatocellular carcinoma, is the most common chronic liver disease worldwide. NAFLD has been considerated to be associated with the composition of gut microbiota. However, causal relationship between change of gut microbiome and NAFLD remains unclear. Here we show that Klebsiella pneumoniae was significantly associated with NAFLD through inducing generation of endogenous ethanol. A strain of high alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) was initially isolated from fecal samples of patient with non-alcoholic steatohepatitis (NASH) accompanied with auto-brewery syndrome (ABS). Gavage of HiAlc Kpn was capable of inducing murine model of fatty liver disease (FLD) in which had typical pathological changes of hepatic steatosis and similar liver gene expression profiles to those of alcohol intake in mice. Data derived from germ-free mice by gnotobiotic gavage further demonstrated that the HiAlc Kpn is the major cause of the changes in FLD mice. Furthermore, using proteomic and metabolitic analysis, we found that HiAlc Kpn induced generation of endogenous alcohol through the 2,3-butanediol fermentation pathway. More interestingly, the blood alcohol concentration was elevated in FLD mice induced by HiAlc Kpn after glucose intake. Clinical analysis showed that HiAlc Kpn were observed in up to 60% of patients with NAFLD. Our results suggested that HiAlc Kpn make important contribution to NAFLD, possibly through generation of the endogenous alcohol. Thus, targeting these bacteria might provide a novel therapeutic for clinical treatment of NAFLD.\n\nIn BriefFatty liver disease induced by high alcohol-producing Klebsiella pneumoniae\n\nCompeting Financial Interest StatementThe authors declare no conflicts of interest.

microbiology↗

bioRxiv2018

High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network

In many normal and abnormal physiological processes, including cellular migration during normal development and invasion in cancer metastasis, cells are required to withstand severe deformations. The structural integrity of eukaryotic cells under small deformations has been known to depend on the cytoskeleton including actin filaments (F-actin), microtubules and intermediate filaments (IFs). However, it remains unclear how cells resist severe deformations since both F-actin and microtubules fluidize or disassemble under moderate strains. Here, we demonstrate that vimentin intermediate filaments (VIFs), a marker of mesenchymal cells, dominate cytoplasmic mechanics at large deformations. Our results show that cytoskeletal VIFs form a stretchable, hyperelastic network. This network works synergistically with other dissipative cytoplasmic components, substantially enhancing the strength, stretchability, resilience and toughness of the living cytoplasm.

biophysics↗

bioRxiv2018

Determination of sex of sacrum in adult Macaca mulatta

[Abstract]O_ST_ABSBackgroundC_ST_ABSSacrum being a part of pelvis is an important bone for identification of sex in both living primates and fossil ones.\n\nAimAim of this work was to examine the sex differences of sacral parameters in rhesus macaques and to compare with those of the other primates.\n\nMaterials and MethodsFifty-six adult scara of macaques (17 males and 39 females) have been investigated. Measurement of various parameters was done using sliding vernier calliper; and statistical analysis was done using SPSS 23.0 package.\n\nResultsThe present study showed that the cranial breadth of the sacrum, the sacral length, transverse diameter and sagittal diameter of the cranial articular surface, and two indices of relative sacral breadth were highly significant for sex determination in Macaca mulatta. Comparison of the present data with other studies suggest that sex determination of sacrum can be very different in various types of primates.\n\nConclusionThe results suggest that these measures may be functionally integrated in response to locomotion, obstetric adequacy and cephalopelvic proportions in primates. Sacral index is more reliable and should be applied for sex determination of sacrum in various anatomical and anthropological investigations.

animal behavior and cognition↗

bioRxiv2018

High-glucose Induces Retinal Pigment Epithelium Mitochondrial Pathways of Apoptosis and Inhibits Mitophagy by Regulating ROS/PINK1/Parkin Signal Pathway

Diabetic retinopathy (DR) caused visual performance degradation seriously endangers human beings health, uncovering the underlying mechanism might shed light on the discovery of DR therapeutic treatments. In this study, we found that the effects of glucose on retinal pigment epithelium (RPE) varies in a dose dependent manner, high-glucose promotes ROS generation and cell apoptosis, inhibits mitophagy as well as proliferative abilities, while low-glucose induces ROS production and cell mitophagy, but has little impacts on cell apoptosis and proliferation. Of note, the toxic effects of high-glucose on RPE are alleviated by ROS scavengers and aggravated by autophagy inhibitor 3-methyladenine (3-MA) or mitophagy inhibitor cyclosporin A (CsA). High-glucose induced ROS generation is merely eliminated by ROS scavengers instead of mitophagy or autophagy inhibitor. We also proved that high-glucose inhibits cell proliferation and promotes cell apoptosis by regulating ROS mediated inhibition of mitophagy. In addition, mitophagy associated proteins PINK1 and Parkin are downregulated by high-glucose or hydrogen peroxide treatments, which are reversed by ROS scavengers. Of note, Knock-down of PINK1 decreases phospharylated Parkin instead of total Parkin levels in RPE. Intriguingly, high-glucoses inhibiting effects on cell mitophagy as well as proliferation and its promoting effects on cell apoptosis are reversed by either PINK1 or Parkin overexpression. Therefore, we concluded that high-glucose promotes RPE apoptosis and inhibits cell proliferation as well as mitophagy by regulating oxidative stress mediated inactivation of ROS/PINKl/Parkin signal pathway.

cell biology↗

bioRxiv2018

The role of BMP6 in the proliferation and differentiation of chicken cartilage cells

Previous studies have indicated that bone morphogenetic protein (BMP) 6 plays an important role in skeletal system development and progression. However, the mechanism underlying the effects of BMP6 in cartilage cell proliferation and differentiation remains unknown. In this study, cartilage cells were isolated from shanks of chicken embryos and treated with different concentrations of GH. Cell proliferation and differentiation potential was assessed using real-time polymerase chain reaction (RT-PCR) and CCK-8 assays in vitro. The results showed that at 48 h, the Collagen II and BMP6 expression levels in 50 ng/l GH-treated cartilage cells were significantly higher than in groups treated with 100 ng/l or 200 ng/l GH. We further observed that knockdown of BMP6 in cartilage cells led to significantly decreased expression levels of Collagen II and Collagen X. Moreover, the suppression of BMP6 expression by a specific siRNA vector led to significantly decreased expression levels of IGF1R, JAK, PKC, PTH, IHH and PTHrP. Taken together, our data suggest that BMP6 may play a critical role in chicken cartilage cell proliferation and differentiation through the regulation of IGF1, JAK2, PKC, PTH, and Ihh-PTHrP signaling pathways.

cell biology↗

bioRxiv2018

Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq

The tumor microenvironment is composed of numerous cell types, including tumor, immune and stromal cells. Cancer cells interact with the tumor microenvironment to suppress anticancer immunity. In this study, we molecularly dissected the tumor microenvironment of breast cancer by single-cell RNA-seq. We profiled the breast cancer tumor microenvironment by analyzing the single-cell transcriptomes of 52,163 cells from the tumor tissues of 15 breast cancer patients. The tumor cells and immune cells from individual patients were analyzed simultaneously at the single-cell level. This study explores the diversity of the cell types in the tumor microenvironment and provides information on the mechanisms of escape from clearance by immune cells in breast cancer.\n\nOne Sentence SummaryLandscape of tumor cells and immune cells in breast cancer by single cell RNA-seq

cancer biology↗

bioRxiv2018

3’ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3’OH Ends in DNA or RNA

Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various molecular tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to join 5 phosphorylated blunt-end double-stranded DNA to DNA breaks at 3 recessive ends, gaps, or nicks to form a 3 branch structure. Therefore, this base pairing-independent ligation is termed 3 branch ligation (3BL). In an extensive study of optimal ligation conditions, similar to blunt-end ligation, the presence of 10% PEG-8000 in the ligation buffer significantly increased ligation efficiency. A low level of nucleotide preference was observed at the junction sites using different synthetic DNAs. Furthermore, we discovered that T4 DNA ligase efficiently ligated DNA to the 3 recessed end of RNA, not to that of DNA, in a DNA/RNA hybrid, whereas RNA ligases are less efficient in this reaction. These novel properties of T4 DNA ligase can be utilized as a broad molecular technique in many important applications. We performed a proof-of-concept study of a new directional tagmentation protocol for next generation sequencing (NGS) library construction that eliminates inverted adapters and allows sample barcode insertion adjacent to genomic DNA. 3BL after single transposon tagmentation can theoretically achieve 100% usable template, and our empirical data demonstrate that the new approach produced higher yield compared with traditional double transposon or Y transposon tagmentation. We further explore the potential use of 3BL for preparing targeted RNA NGS libraries with mitigated structure-based bias and adapter dimer problems.

molecular biology↗

bioRxiv2018

Bats adjust temporal features of echolocation calls but not those of communication calls in response to traffic noise

Summary statementThis study reveals the impact of anthropogenic noise on spectrally distinct vocalizations and the limitations of the acoustic masking hypothesis to explain the vocal response of bats to chronic noise.\n\nAbstractThe acoustic masking hypothesis states that auditory masking may occur if the target sound and interfering sounds overlap spectrally, and it suggests that animals exposed to noise will modify their acoustic signals to increase signal detectability. However, it is unclear if animals will put more effort into changing their signals that spectrally overlap more with the interfering sounds than when the signals overlap less. We examined the dynamic changes in the temporal features of echolocation and communication vocalizations of the Asian particolored bat (Vespertilio sinensis) when exposed to traffic noise. We hypothesized that traffic noise has a greater impact on communication vocalizations than on echolocation vocalizations and predicted that communication vocalization change would be greater than echolocation. The bats started to adjust echolocation vocalizations on the fourth day of noise exposure, including an increased number of call sequences, decreased number of calls, and vocal rate within a call sequence. However, there was little change in the duration of the call sequence. In contrast, these communication vocalization features were not significantly adjusted under noise conditions. These findings suggest that the degree of spectral overlap between noise and animal acoustic signals does not predict the level of temporal vocal response to the noise.

animal behavior and cognition↗

bioRxiv2018

Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

BackgroundMassively-parallel-sequencing, coupled with sample multiplexing, has made genetic tests broadly affordable. However, intractable index mis-assignments (commonly exceeds 1%) were repeatedly reported on some widely used sequencing platforms.\n\nResultsHere, we investigated this quality issue on BGI sequencers using three library preparation methods: whole genome sequencing (WGS) with PCR, PCR-free WGS, and two-step targeted PCR. BGIs sequencers utilize a unique DNB technology which uses rolling circle replication for DNA-nanoball preparation; this linear amplification is PCR free and can avoid error accumulation. We demonstrated that single index mis-assignment from free indexed oligos occurs at a rate of one in 36 million reads, suggesting virtually no index hopping during DNB creation and arraying. Furthermore, the DNB-based NGS libraries have achieved an unprecedentedly low sample-to-sample mis-assignment rate of 0.0001% to 0.0004% under recommended procedures.\n\nConclusionsSingle indexing with DNB technology provides a simple but effective method for sensitive genetic assays with large sample numbers.

genomics↗

bioRxiv2018

Trio deep-sequencing does not reveal unexpected mutations in Cas9-edited monkeys

CRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect remains a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, no comprehensive in vivo off-target assessment has been conducted in NHPs. Here we performed whole genome trio sequencing of Cas9-treated monkeys. We found they only carried a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected mutations were detected.

bioengineering↗